BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234052.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,579,303 number of mapped reads = 2,450,314 (95%) number of supplementary alignments = 15,194 (0.59%) number of secondary alignments = 0 number of mapped bases = 164,219,428 bp number of sequenced bases = 164,136,203 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 169,705 duplication rate = 5.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7815 >>>>>>> ACTG content number of A's = 44,461,958 bp (27.09%) number of C's = 30,547,442 bp (18.61%) number of T's = 52,201,166 bp (31.8%) number of G's = 36,909,430 bp (22.49%) number of N's = 16,207 bp (0.01%) GC percentage = 41.1% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,065,392 number of insertions = 12,911 mapped reads with insertion percentage = 0.52% number of deletions = 48,820 mapped reads with deletion percentage = 1.97% homopolymer indels = 45.14% >>>>>>> Coverage mean coverageData = 0.053X std coverageData = 0.6231X There is a 4.5% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8144895 0.03267753142328179 1.5145199899045714 chr2 243199373 13778061 0.05665335740812128 0.6220372277207711 chr3 198022430 22327476 0.11275225740841581 0.3816509163001515 chr4 191154276 8643158 0.04521561421937535 0.2505070648524836 chr5 180915260 9631103 0.053235437408651984 0.2640818580639033 chr6 171115067 9288973 0.05428495083954238 0.45506719239062227 chr7 159138663 8220778 0.051657955678564425 0.6375223201851115 chr8 146364022 6355428 0.043422064474287266 0.7722982348344558 chr9 141213431 7203575 0.05101196783470264 0.4239218952652209 chr10 135534747 5449832 0.04020985113138552 0.5618954722778815 chr11 135006516 9405425 0.06966645224738634 0.5369644820566931 chr12 133851895 5019062 0.037497130690603966 0.23411436568097632 chr13 115169878 5858182 0.05086557441694954 0.2611806676406296 chr14 107349540 6634791 0.06180549073615034 0.30634788124703444 chr15 102531392 3213754 0.03134409801049029 0.2081166646906731 chr16 90354753 4131384 0.04572403623304687 0.29573083905983594 chr17 81195210 4687675 0.05773339338613694 0.3475555016577226 chr18 78077248 2964800 0.03797264985569163 0.8955799677818996 chr19 59128983 5990328 0.10130950501888389 0.8727905818317698 chr20 63025520 4034107 0.06400751632037308 0.2987100175126908 chr21 48129895 2532148 0.052610711076764245 0.27867963638601334 chr22 51304566 1028922 0.020055174036556513 0.15763446932462213 chrMT 16571 157696 9.516384044414941 6.1080255112233175 chrX 155270560 9149680 0.058927333037248016 0.3397954323557949 chrY 59373566 368195 0.0062013287192485625 0.12648737938744284